Associations of the Expression Levels and Risk Variants of CDKN2B-AS1 Long Noncoding RNA With the Susceptibility and Progression of Prostate Cancer

Abstract

Genetic variants of deregulated long noncoding RNAs (lncRNAs) have been implicated in tumorigenesis, cancer progression and cancer recurrence. Single-nucleotide polymorphisms (SNPs) of the lncRNA cyclin-dependent kinase inhibitor 2B antisense RNA 1 (CDKN2B-AS1) have been associated with the risk and progression of various cancers; however, their role in prostate cancer (PCa) remains underexplored. In this case-control study, we investigated the associations of CDKN2B-AS1 expression levels and variants with PCa risk and progression. For this, five SNPs of CDKN2B-AS1-rs564398, rs1333048, rs1537373, rs2151280 and rs8181047-were genotyped using a TaqMan allelic discrimination assay; data were collected from 695 patients with PCa and 695 healthy controls. Our findings revealed that, under a dominant model, patients with PCa carrying at least one minor C allele of rs1333048 exhibited an increased risk of developing tumours with high Gleason grades; this risk was particularly high in patients without biochemical recurrence. Data from the Genotype-Tissue Expression database indicated upregulated CDKN2B-AS1 expression in the prostates of individuals carrying the polymorphic C allele of rs1333048. Genotype screening of rs1333048 in PCa cell lines showed that cells with at least one minor C allele had higher CDKN2B-AS1 levels than those with the AA genotype. Furthermore, data from The Cancer Genome Atlas indicated that higher CDKN2B-AS1 levels in PCa tissues were correlated with larger tumour sizes (T3 + T4), more lymph node metastasis (N1), higher Gleason scores and shorter progression-free survival. In conclusion, the polymorphic variants of CDKN2B-AS1 at rs1333048 may modulate CDKN2B-AS1 expression, thus accelerating PCa progression.

Keywords: cancer progression; cancer susceptibility; cyclin‐dependent kinase inhibitor 2B antisense RNA 1; long noncoding RNA; prostate cancer; single‐nucleotide polymorphism.

FIGURE 1

Impacts of CDKN2B‐AS1 rs1333048 polymorphisms on CDKN2B‐AS1 expression. (A) The Genotype Tissue Expression (GTEx) Portal (https://www.gtexportal.org/home/) provided data on CDKN2B‐AS1 expression across different genotypes. The violin plot shows that the C allele of rs1333048 tends to be associated with higher CDKN2B‐AS1 expression levels in prostate tissue. (B) Correlation between CDKN2B‐AS1 rs1333048 genotypes and CDKN2B‐AS1 expression levels was examined in four prostate cancer (PCa) cell lines. In the lower panel, CDKN2B‐AS1 rs1333048 genotypes in PCa cells (PC3, PC3‐M, DU145 and 22Rv1) were identified using a TaqMan SNP Genotyping Assay, while the upper panel shows CDKN2B‐AS1 expression levels determined by RT‐qPCR. Differences are presented as mean ± standard deviation. ***p < 0.001, compared to PC3 cells; # p < 0.05, ## p < 0.01, compared to PC3‐M cells.

FIGURE 2

Clinical significance of CDKN2B‐AS1 expression levels in patients with prostate cancer (PCa). The clinical significance was analysed using data from The Cancer Genome Atlas Prostate Adenocarcinoma dataset. (A) CDKN2B‐AS1 expression in normal versus PCa tissues. (B and C) Expression levels of CDKN2B‐AS1 in PCa patients stratified by Gleason scores (B) and pathological T stage and lymph node metastasis (C). (D) Kaplan–Meier curves indicating progression‐free survival in patients with high or low levels of CDKN2B‐AS1 expression (CDKN2B‐AS1 ^high and CDKN2B‐AS1 ^low, respectively). The p values indicate the significance of difference between the two expression groups.

FIGURE 3

CDKN2B‐AS1‐associated pathways in patients with prostate cancer (PCa). (A) A horizontal bar plot indicating the pathways associated with CDKN2B‐AS1. Red and blue bars indicate pathways positively and negatively, respectively, associated with CDKN2B‐AS1. The x‐axis presents the normalised enrichment scores (NES), whereas the y‐axis presents the pathways identified from the Hallmark database. (B and C) Correlation plots indicating the correlations of CDKN2B‐AS1 expression with the biomarkers of epithelial–mesenchymal transition (B) and those of inflammatory response (C). RNA sequencing data from The Cancer Genome Atlas Prostate Adenocarcinoma dataset were analysed. Pearson correlation analysis was performed to identify the correlations between CDKN2B‐AS1 and the aforementioned biomarkers. Correlation coefficients and p values are presented in each square, with the scale bar representing the strength of correlation.